In nature plants live in a balanced relationship with microorganisms.

Plants do not have the ability to remove nutrients from soil, but bacteria and fungi do. Plants will excrete simple sugars into the soil to feed bacteria and fungi. Bacteria and fungi will then break down organic matter and soil particles to release the nutrients stored inside these structures. These nutrients are then stored inside the bodies of bacteria and fungi. When predatory organisms consume bacteria and fungi the nutrients are released in a plant available form within their waste products. The plants are able to easily absorb all the nutrients they need from these waste products.

This results in well nourished, resilient plants and nutrient dense foods for humans, free from chemicals.

Bacteria produce glues to adhere to organic matter and soil particles. These particles then glue together forming microaggregate.

Fungi grow like ropes through the soil, pulling together these microaggregates and creating macroaggregates. In this manner larger spaces are created in the soil. Microarthropods, earthworms and insects burrow through the soil creating tunnels, contributing to the structure.

Surface litter will be decomposed into humus by the soil food web and transported deeper into the soil.

This increase in organic matter as well as good structure acts like a sponge and are able to hold water for several months.

With improved structure roots are able to grow deeper and access more water and nutrients in the soil.

Excess water can flow through the soil increasing resistance to soil erosion by water. A well-structured soil is also more resistant to wind erosion.

In natural soils, free from fertilizer, the type of nitrogen that is excreted by predatory organisms is ammonium. A certain type of bacteria, called nitrifying bacteria, will convert ammonium into nitrates. Most plants require a combination of nitrate and ammonium. Weeds will thrive in a soil that is rich in nitrates.
Nitrifying bacteria can only operate in a pH above 7. The beneficial fungi found in a balanced soil food web will produce acidic compounds that prevents the pH from reaching 7 and nitrifying bacteria are unable to convert ammonium into nitrate.
With less nitrate in the soil weeds are kept under control.

Most disease-causing organisms thrive in low oxygen conditions.
A well-structured soil will create an oxygen rich environment, inhibiting disease causing organisms.
When plants excrete sugars from roots as well as stems and leaves, the entire plant become completely covered in beneficial organisms. This makes it difficult for disease causing organisms to get access to the plant surface. Predatory organisms also consume these disease-causing organisms.
Healthy plants produce chemicals that deter pests. Sick plants are unable to produce these chemicals and are more susceptible to attack.

During photosynthesis plants absorb carbon from the atmosphere and produce simple sugars and other related compounds.

About 40% of these carbon-rich compounds (exudates) are excreted into the soil, in order to feed bacteria and fungi. 

Fungi grow in long tube-like structures called hypha. Fungal hypha is mostly made of carbon. In this manner carbon is stored within the fungi. Fungi will grow longer and branch in different directions looking for new food resources. Over time its walls grow thicker, storing more and more carbon. This process is called soil carbon sequestration.